We identified neighbouring genes based on the RefSeq genome annotation57 (NCBI Release 39). We excluded from analysis all RefSeq genes that corresponded to our lincRNA of interest but included all other coding and non-coding transcripts. We identified a significant hit as any lincRNA affecting a neighbour within 10 genes on either side with an FDR<.05 and 2-fold expression change. To compute the closest affected neighbour, we classified all genes affected upon knockdown of the lincRNAs using the same criteria above. We computed the distance between each affected gene and the locus of the lincRNA gene (and protein-coding gene) that was perturbed and took the minimum absolute distance across all affected genes.
